inprogress

[jalview.git] / forester / java / src / org / forester / test / examples / Example4.java

diff --git a/forester/java/src/org/forester/test/examples/Example4.java b/forester/java/src/org/forester/test/examples/Example4.java
index b363ab3..7f35850 100644 (file)
--- a/forester/java/src/org/forester/test/examples/Example4.java
+++ b/forester/java/src/org/forester/test/examples/Example4.java
@@ -22,7 +22,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.test.examples;
 
@@ -30,8 +30,10 @@ import java.io.File;
 import java.io.IOException;
 
 import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.util.ParserUtils;
 import org.forester.io.writers.PhylogenyWriter;
 import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.util.ForesterUtil;
 
 public class Example4 {
@@ -41,14 +43,14 @@ public class Example4 {
         final File treefile = new File( "/home/czmasek/tol_117_TEST.xml" );
         PhylogenyParser parser = null;
         try {
-            parser = ForesterUtil.createParserDependingOnFileType( treefile, true );
+            parser = ParserUtils.createParserDependingOnFileType( treefile, true );
         }
         catch ( final IOException e ) {
             e.printStackTrace();
         }
         Phylogeny[] phys = null;
         try {
-            phys = ForesterUtil.readPhylogenies( parser, treefile );
+            phys = PhylogenyMethods.readPhylogenies( parser, treefile );
         }
         catch ( final IOException e ) {
             e.printStackTrace();